rs334543

chr3-120113774-C-Achr3-120113774-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484076.1(GSK3B-DT):n.415+8929C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,046 control chromosomes in the GnomAD database, including 42,069 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42069 hom., cov: 31)
• Consequence: GSK3B-DT ENST00000484076.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

Genes affected

GSK3B-DT (HGNC:55635): (GSK3B divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSK3B-DT	ENST00000484076.1	n.415+8929C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112155 AN: 151928 Hom.: 42021 Cov.: 31

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.713

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.738 AC: 112247 AN: 152046 Hom.: 42069 Cov.: 31 AF XY: 0.736 AC XY: 54678 AN XY: 74316

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.714

Alfa AF: 0.697 Hom.: 51096

Bravo AF: 0.732

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	8.1
Dann	Benign	0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs334543; hg19: chr3-119832621;